If you export as PDF or SVG, you should get a scalar graphic with high
resolution lines. If you try PDF or SVG and still do not see lines,
please send the .cys and image file so we can try to reproduce error.
I noticed you said "some lines". This makes me think perhaps you were
working with a pathway network from WikiPathways and the lines that
are not edges (connecting nodes) are the ones that were missing. Is
this the case? Again, sending examples would help.
- Alex